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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ptairMS_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ptairMS.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ptairMS/DESCRIPTION’ ... OK
* this is package ‘ptairMS’ version ‘1.4.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ptairMS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: undefined slot classes in definition of "ptrRaw": peakList(class "ExpressionSet")
See ‘/Users/biocbuild/bbs-3.15-bioc/meat/ptairMS.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getCalibrationInfo’ ‘getPeakList’ ‘getPeaksInfo’ ‘getTimeInfo’
  ‘processFileTemporalNominalMass’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
detectPeak           154.517  2.323 157.075
alignSamples          28.242  0.954  29.264
imputeMat             26.149  0.765  27.086
writeEset             23.720  0.602  24.351
annotation            23.559  0.593  24.179
impute                23.177  0.667  23.876
getPeakList           22.663  0.556  23.243
plot                  20.381  0.369  21.508
plotTIC               20.079  0.486  21.277
plotRaw               18.175  0.507  19.451
plotFeatures          17.837  0.476  18.411
plotCalib             17.298  0.352  18.793
rmPeakList            17.258  0.386  18.652
resetSampleMetadata   17.237  0.291  18.503
setSampleMetadata     16.283  0.363  16.895
exportSampleMetada    15.512  0.332  15.876
getSampleMetadata     15.370  0.338  15.723
getDirectory          15.206  0.349  15.572
defineKnots           15.006  0.340  15.375
getFileNames          14.877  0.376  15.277
updatePtrSet          14.890  0.305  15.228
importSampleMetadata  14.785  0.329  15.130
createPtrSet          13.848  0.419  14.301
changeTimeLimits      13.741  0.313  14.081
convert_to_mzML        9.806  0.217  10.035
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/ptairMS.Rcheck/00check.log’
for details.